Author: bugman
Date: Thu May 30 18:40:10 2013
New Revision: 19800
URL: http://svn.gna.org/viewcvs/relax?rev=19800&view=rev
Log:
Updated the relax_disp.exp_type user function to be more specific an include
more experiment types.
Modified:
branches/relax_disp/specific_analyses/relax_disp/__init__.py
branches/relax_disp/user_functions/relax_disp.py
Modified: branches/relax_disp/specific_analyses/relax_disp/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp/__init__.py?rev=19800&r1=19799&r2=19800&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/__init__.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/__init__.py Thu May 30
18:40:10 2013
@@ -265,38 +265,34 @@
return ids
- def _exp_type(self, exp_type='cpmg'):
+ def _exp_type(self, exp_type='cpmg fixed'):
"""Select the relaxation dispersion experiment type performed.
- @keyword exp: The relaxation dispersion experiment type. Can be one
of 'cpmg' or 'r1rho'.
+ @keyword exp: The relaxation dispersion experiment type. Can be one
of 'cpmg fixed', 'cpmg exponential', 'r1rho fixed' or 'r1rho exponential'.
@type exp: str
"""
# Test if the current pipe exists.
pipes.test()
- # CPMG relaxation dispersion experiments (exponential curves with
varying relax_T).
- if exp_type == 'cpmg':
- print("CPMG experiments with exponential curves from varying the
relaxation period.")
- cdp.exp_type = 'cpmg'
-
- # CPMG relaxation dispersion experiments (fixed relax_T).
- elif exp_type == 'cpmg fixed':
- print("CPMG experiments with a fixed relaxation period.")
- cdp.exp_type = 'cpmg fixed'
-
- # R1rho relaxation dispersion experiments.
- elif exp_type == 'r1rho':
- print("R1rho experiments with exponential curves from varying
the time of application of the spin-lock field.")
- cdp.exp_type = 'r1rho'
-
- # Invalid relaxation dispersion experiment.
+ # Printouts.
+ if exp_type == 'cpmg fixed':
+ print("The fixed relaxation time period CPMG-type experiments.")
+ elif exp_type == 'cpmg exponential':
+ print("The CPMG-type experiments consisting of full exponential
curves for each dispersion point.")
+ elif exp_type == 'r1rho fixed':
+ print("The fixed relaxation time period R1rho-type experiments.")
+ elif exp_type == 'r1rho exponential':
+ print("The R1rho-type experiments consisting of full exponential
curves for each dispersion point.")
else:
raise RelaxError("The relaxation dispersion experiment '%s' is
invalid." % exp_type)
# Sanity check.
if exp_type not in FIXED_TIME_EXP and exp_type not in VAR_TIME_EXP:
raise RelaxError("The experiment type '%s' is neither a fixed
relaxation time period or variable relaxation time period experiment." %
exp_type)
+
+ # Store the value.
+ cdp.exp_type = exp_type
def _grid_search_setup(self, spins=None, param_vector=None, lower=None,
upper=None, inc=None, scaling_matrix=None):
Modified: branches/relax_disp/user_functions/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/user_functions/relax_disp.py?rev=19800&r1=19799&r2=19800&view=diff
==============================================================================
--- branches/relax_disp/user_functions/relax_disp.py (original)
+++ branches/relax_disp/user_functions/relax_disp.py Thu May 30 18:40:10 2013
@@ -225,42 +225,53 @@
uf.title_short = "Relaxation dispersion experiment type selection."
uf.add_keyarg(
name = "exp_type",
- default = "cpmg",
+ default = "cpmg fixed",
py_type = "str",
desc_short = "experiment type",
desc = "The type of relaxation dispersion experiment performed.",
wiz_element_type = "combo",
wiz_combo_choices = [
- "CPMG",
"CPMG, fixed time",
- "R1rho"
+ "CPMG, full exponential",
+ "R1rho, fixed time",
+ "R1rho, full exponential"
],
wiz_combo_data = [
- "cpmg",
"cpmg fixed",
- "r1rho"
+ "cpmg exponential",
+ "r1rho fixed",
+ "r1rho exponential"
],
wiz_read_only = True
)
# Description.
uf.desc.append(Desc_container())
uf.desc[-1].add_paragraph("The currently supported experiments include:")
-uf.desc[-1].add_item_list_element("'cpmg'", "The CPMG family of experiments
whereby spectra consist of exponential curves by varying the total time of
the CPMG block of pulses,")
-uf.desc[-1].add_item_list_element("'cpmg fixed'", "The CPMG family of
experiments whereby the time period for the block of CPMG pulses is fixed and
a reference spectrum is present,")
-uf.desc[-1].add_item_list_element("'r1rho'", "The R1rho family of
experiments whereby spectra consist of exponential curves by varying the
total time in which the spin-lock field is applied.")
-uf.desc[-1].add_paragraph("For the 'cpmg' and 'r1rho' experiment types,
2-parameter exponentials will be fit to obtain R2,eff for each spin system as
part of the optimisation of the dispersion model.")
-uf.desc[-1].add_paragraph("For the 'cpmg fixed' experiment type, the R2,eff
values are directly calculated prior to optimisation using the formula:")
+uf.desc[-1].add_item_list_element("'cpmg fixed'", "The fixed relaxation time
period CPMG-type experiments,")
+uf.desc[-1].add_item_list_element("'cpmg exponential'", "The full
exponential curve CPMG-type experiments,")
+uf.desc[-1].add_item_list_element("'r1rho fixed'", "The fixed relaxation
time period R1rho-type experiments,")
+uf.desc[-1].add_item_list_element("'r1rho exponential'", "The full
exponential curve R1rho-type experiments.")
+uf.desc[-1].add_paragraph("For the full exponential curve experiment types,
2-parameter exponentials will be fit to obtain R2eff/R1rho for each spin
system as part of the optimisation of the dispersion model.")
+uf.desc[-1].add_paragraph("For the fixed time period experiment types, the
R2eff/R1rho values are directly calculated prior to optimisation using the
formula:")
uf.desc[-1].add_verbatim("""
- -1 / I1(nu_CPMG) \
- R2,eff(nu_CPMG) = ------- * ln | ----------- |,
- relax_T \ I0 /
-""")
-uf.desc[-1].add_paragraph("where nu_CPMG is the CPMG frequency in Hz,
relax_T is the fixed delay time, I0 is the reference peak intensity when
relax_T is zero, and I1 is the peak intensity in a spectrum for a given
nu_CPMG frequency.")
+ -1 / I1(nu) \
+ R2eff(nu) = ------- * ln | ------ |,
+ relax_T \ I0 /
+""")
+uf.desc[-1].add_paragraph("where nu is either the CPMG frequency in Hz or
the spin-lock field strength in Hz, relax_T is the fixed delay time, I0 is
the reference peak intensity when relax_T is zero, and I1 is the peak
intensity in a spectrum for a given nu_CPMG frequency. The error is
calculated with the formula:")
+uf.desc[-1].add_verbatim("""
+ _____________________________________
+ 1 / / sigma_I0 \ 2 / sigma_I1(nu) \ 2
+ sigma(nu) = ------- * \ / | -------- | + | ------------ |
+ relax_T \/ \ I0 / \ I1 /
+
+""")
+uf.desc[-1].add_paragraph("where sigma is the standard deviation.")
# Prompt examples.
uf.desc.append(Desc_container("Prompt examples"))
-uf.desc[-1].add_paragraph("To pick the experiment type 'cpmg' for all
selected spins, type one of:")
-uf.desc[-1].add_prompt("relax> relax_disp.exp_type('cpmg')")
-uf.desc[-1].add_prompt("relax> relax_disp.exp_type(exp_type='cpmg')")
+uf.desc[-1].add_paragraph("To pick the experiment type 'cpmg fixed' for all
selected spins, type one of:")
+uf.desc[-1].add_prompt("relax> relax_disp.exp_type('cpmg fixed')")
+uf.desc[-1].add_prompt("relax> relax_disp.exp_type(exp_type='cpmg fixed')")
uf.backend = relax_disp_obj._exp_type
uf.menu_text = "&exp_type"
uf.wizard_height_desc = 500
r19800 - in /branches/relax_disp: specific_analyses/relax_disp/__init__.py user_functions/relax_disp.py